vcf_clone_detect.py results for P. acuta RNA-seq samples from this study and SRASetup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 12,
fig.width = 12,
dev = c("png", "pdf"),
dpi = 1000)
library(readxl)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
library(reshape2)
library(RcppCNPy)
library(tibble)
library(ggdendro)
library(cowplot)
library(RColorBrewer)
library(viridis)
## Loading required package: viridisLite
library(knitr)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(phylogram)
options(scipen = 999) #Prevent scientific notation
cexSize <- 0.3
Load file with annotation for each sample.
samples.info <- read.table("../../../samples_Pacuta_ALL.annotations.txt", header=T, comment.char='')
rownames(samples.info) <- samples.info$sample
samples.info
## sample species treatment
## Pacuta_ATAC_TP11_1777 Pacuta_ATAC_TP11_1777 Pacuta ATAC
## Pacuta_ATAC_TP8_1051 Pacuta_ATAC_TP8_1051 Pacuta ATAC
## Pacuta_ATHC_TP4_2733 Pacuta_ATHC_TP4_2733 Pacuta ATHC
## Pacuta_ATHC_TP8_1459 Pacuta_ATHC_TP8_1459 Pacuta ATHC
## Pacuta_HTAC_TP3_1642 Pacuta_HTAC_TP3_1642 Pacuta HTAC
## Pacuta_HTAC_TP4_1767 Pacuta_HTAC_TP4_1767 Pacuta HTAC
## Pacuta_HTAC_TP7_2072 Pacuta_HTAC_TP7_2072 Pacuta HTAC
## Pacuta_ATAC_TP11_1103 Pacuta_ATAC_TP11_1103 Pacuta ATAC
## Pacuta_ATAC_TP11_2306 Pacuta_ATAC_TP11_2306 Pacuta ATAC
## Pacuta_ATAC_TP3_1041 Pacuta_ATAC_TP3_1041 Pacuta ATAC
## Pacuta_ATAC_TP3_1637 Pacuta_ATAC_TP3_1637 Pacuta ATAC
## Pacuta_ATAC_TP4_1762 Pacuta_ATAC_TP4_1762 Pacuta ATAC
## Pacuta_ATAC_TP7_2413 Pacuta_ATAC_TP7_2413 Pacuta ATAC
## Pacuta_ATAC_TP8_2012 Pacuta_ATAC_TP8_2012 Pacuta ATAC
## Pacuta_ATAC_TP9_2357 Pacuta_ATAC_TP9_2357 Pacuta ATAC
## Pacuta_ATHC_TP11_1147 Pacuta_ATHC_TP11_1147 Pacuta ATHC
## Pacuta_ATHC_TP3_2534 Pacuta_ATHC_TP3_2534 Pacuta ATHC
## Pacuta_ATHC_TP4_1220 Pacuta_ATHC_TP4_1220 Pacuta ATHC
## Pacuta_ATHC_TP5_2877 Pacuta_ATHC_TP5_2877 Pacuta ATHC
## Pacuta_ATHC_TP6_2870 Pacuta_ATHC_TP6_2870 Pacuta ATHC
## Pacuta_ATHC_TP7_2878 Pacuta_ATHC_TP7_2878 Pacuta ATHC
## Pacuta_ATHC_TP9_1451 Pacuta_ATHC_TP9_1451 Pacuta ATHC
## Pacuta_ATHC_TP9_2873 Pacuta_ATHC_TP9_2873 Pacuta ATHC
## Pacuta_HTAC_TP10_2064 Pacuta_HTAC_TP10_2064 Pacuta HTAC
## Pacuta_HTAC_TP11_1596 Pacuta_HTAC_TP11_1596 Pacuta HTAC
## Pacuta_HTAC_TP1_2414 Pacuta_HTAC_TP1_2414 Pacuta HTAC
## Pacuta_HTAC_TP5_1707 Pacuta_HTAC_TP5_1707 Pacuta HTAC
## Pacuta_HTAC_TP6_1466 Pacuta_HTAC_TP6_1466 Pacuta HTAC
## Pacuta_HTAC_TP7_1728 Pacuta_HTAC_TP7_1728 Pacuta HTAC
## Pacuta_HTAC_TP8_2513 Pacuta_HTAC_TP8_2513 Pacuta HTAC
## Pacuta_HTAC_TP9_1696 Pacuta_HTAC_TP9_1696 Pacuta HTAC
## Pacuta_HTHC_TP10_2300 Pacuta_HTHC_TP10_2300 Pacuta HTHC
## Pacuta_HTHC_TP3_1227 Pacuta_HTHC_TP3_1227 Pacuta HTHC
## Pacuta_HTHC_TP5_2087 Pacuta_HTHC_TP5_2087 Pacuta HTHC
## Pacuta_HTHC_TP6_1138 Pacuta_HTHC_TP6_1138 Pacuta HTHC
## Pacuta_HTHC_TP6_1595 Pacuta_HTHC_TP6_1595 Pacuta HTHC
## Pacuta_HTHC_TP8_1709 Pacuta_HTHC_TP8_1709 Pacuta HTHC
## Pacuta_HTHC_TP8_2304 Pacuta_HTHC_TP8_2304 Pacuta HTHC
## Pacuta_HTHC_TP9_1131 Pacuta_HTHC_TP9_1131 Pacuta HTHC
## Pacuta_HTHC_TP9_2202 Pacuta_HTHC_TP9_2202 Pacuta HTHC
## Pacuta_HTHC_TP9_2305 Pacuta_HTHC_TP9_2305 Pacuta HTHC
## Pacuta_ATAC_TP10_1559 Pacuta_ATAC_TP10_1559 Pacuta ATAC
## Pacuta_ATAC_TP10_1641 Pacuta_ATAC_TP10_1641 Pacuta ATAC
## Pacuta_ATAC_TP1_2363 Pacuta_ATAC_TP1_2363 Pacuta ATAC
## Pacuta_ATAC_TP3_1471 Pacuta_ATAC_TP3_1471 Pacuta ATAC
## Pacuta_ATAC_TP4_1060 Pacuta_ATAC_TP4_1060 Pacuta ATAC
## Pacuta_ATAC_TP4_2002 Pacuta_ATAC_TP4_2002 Pacuta ATAC
## Pacuta_ATAC_TP5_1563 Pacuta_ATAC_TP5_1563 Pacuta ATAC
## Pacuta_ATAC_TP5_1757 Pacuta_ATAC_TP5_1757 Pacuta ATAC
## Pacuta_ATAC_TP9_1594 Pacuta_ATAC_TP9_1594 Pacuta ATAC
## Pacuta_ATHC_TP7_2409 Pacuta_ATHC_TP7_2409 Pacuta ATHC
## Pacuta_ATHC_TP8_2564 Pacuta_ATHC_TP8_2564 Pacuta ATHC
## Pacuta_HTAC_TP10_1536 Pacuta_HTAC_TP10_1536 Pacuta HTAC
## Pacuta_HTAC_TP11_1582 Pacuta_HTAC_TP11_1582 Pacuta HTAC
## Pacuta_HTAC_TP11_1647 Pacuta_HTAC_TP11_1647 Pacuta HTAC
## Pacuta_HTAC_TP1_2005 Pacuta_HTAC_TP1_2005 Pacuta HTAC
## Pacuta_HTAC_TP3_1617 Pacuta_HTAC_TP3_1617 Pacuta HTAC
## Pacuta_HTAC_TP4_1701 Pacuta_HTAC_TP4_1701 Pacuta HTAC
## Pacuta_HTAC_TP8_1765 Pacuta_HTAC_TP8_1765 Pacuta HTAC
## Pacuta_HTHC_TP10_1238 Pacuta_HTHC_TP10_1238 Pacuta HTHC
## Pacuta_HTHC_TP10_1732 Pacuta_HTHC_TP10_1732 Pacuta HTHC
## Pacuta_HTHC_TP1_1239 Pacuta_HTHC_TP1_1239 Pacuta HTHC
## Pacuta_HTHC_TP4_2195 Pacuta_HTHC_TP4_2195 Pacuta HTHC
## Pacuta_HTHC_TP7_1090 Pacuta_HTHC_TP7_1090 Pacuta HTHC
## Pacuta_HTHC_TP7_1820 Pacuta_HTHC_TP7_1820 Pacuta HTHC
## Pacuta_ATAC_TP1_1043 Pacuta_ATAC_TP1_1043 Pacuta ATAC
## Pacuta_ATAC_TP6_1542 Pacuta_ATAC_TP6_1542 Pacuta ATAC
## Pacuta_ATHC_TP1_2743 Pacuta_ATHC_TP1_2743 Pacuta ATHC
## Pacuta_ATHC_TP3_2750 Pacuta_ATHC_TP3_2750 Pacuta ATHC
## Pacuta_HTAC_TP4_1581 Pacuta_HTAC_TP4_1581 Pacuta HTAC
## Pacuta_HTHC_TP4_1343 Pacuta_HTHC_TP4_1343 Pacuta HTHC
## Pacuta_HTHC_TP7_1427 Pacuta_HTHC_TP7_1427 Pacuta HTHC
## Pacuta_HTHC_TP8_1184 Pacuta_HTHC_TP8_1184 Pacuta HTHC
## Pacuta_ATAC_TP10_1159 Pacuta_ATAC_TP10_1159 Pacuta ATAC
## Pacuta_ATAC_TP1_1775 Pacuta_ATAC_TP1_1775 Pacuta ATAC
## Pacuta_ATAC_TP6_1468 Pacuta_ATAC_TP6_1468 Pacuta ATAC
## Pacuta_ATAC_TP8_1755 Pacuta_ATAC_TP8_1755 Pacuta ATAC
## Pacuta_ATAC_TP9_1141 Pacuta_ATAC_TP9_1141 Pacuta ATAC
## Pacuta_ATHC_TP5_2212 Pacuta_ATHC_TP5_2212 Pacuta ATHC
## Pacuta_HTAC_TP6_1744 Pacuta_HTAC_TP6_1744 Pacuta HTAC
## Pacuta_HTAC_TP9_1302 Pacuta_HTAC_TP9_1302 Pacuta HTAC
## Pacuta_HTAC_TP9_1486 Pacuta_HTAC_TP9_1486 Pacuta HTAC
## Pacuta_ATAC_TP6_1050 Pacuta_ATAC_TP6_1050 Pacuta ATAC
## Pacuta_ATAC_TP7_1047 Pacuta_ATAC_TP7_1047 Pacuta ATAC
## Pacuta_ATHC_TP10_2197 Pacuta_ATHC_TP10_2197 Pacuta ATHC
## Pacuta_ATHC_TP1_1207 Pacuta_ATHC_TP1_1207 Pacuta ATHC
## Pacuta_ATHC_TP11_2668 Pacuta_ATHC_TP11_2668 Pacuta ATHC
## Pacuta_ATHC_TP11_2879 Pacuta_ATHC_TP11_2879 Pacuta ATHC
## Pacuta_ATHC_TP1_2977 Pacuta_ATHC_TP1_2977 Pacuta ATHC
## Pacuta_ATHC_TP3_1219 Pacuta_ATHC_TP3_1219 Pacuta ATHC
## Pacuta_ATHC_TP4_2993 Pacuta_ATHC_TP4_2993 Pacuta ATHC
## Pacuta_ATHC_TP5_1296 Pacuta_ATHC_TP5_1296 Pacuta ATHC
## Pacuta_ATHC_TP6_2999 Pacuta_ATHC_TP6_2999 Pacuta ATHC
## Pacuta_ATHC_TP7_1281 Pacuta_ATHC_TP7_1281 Pacuta ATHC
## Pacuta_ATHC_TP8_2861 Pacuta_ATHC_TP8_2861 Pacuta ATHC
## Pacuta_ATHC_TP9_2979 Pacuta_ATHC_TP9_2979 Pacuta ATHC
## Pacuta_HTAC_TP10_1225 Pacuta_HTAC_TP10_1225 Pacuta HTAC
## Pacuta_HTAC_TP3_2026 Pacuta_HTAC_TP3_2026 Pacuta HTAC
## Pacuta_HTAC_TP5_1303 Pacuta_HTAC_TP5_1303 Pacuta HTAC
## Pacuta_HTAC_TP5_1571 Pacuta_HTAC_TP5_1571 Pacuta HTAC
## Pacuta_HTAC_TP6_1330 Pacuta_HTAC_TP6_1330 Pacuta HTAC
## Pacuta_HTAC_TP7_1487 Pacuta_HTAC_TP7_1487 Pacuta HTAC
## Pacuta_HTAC_TP8_1329 Pacuta_HTAC_TP8_1329 Pacuta HTAC
## Pacuta_HTHC_TP11_1416 Pacuta_HTHC_TP11_1416 Pacuta HTHC
## Pacuta_HTHC_TP1_1676 Pacuta_HTHC_TP1_1676 Pacuta HTHC
## Pacuta_HTHC_TP3_1418 Pacuta_HTHC_TP3_1418 Pacuta HTHC
## Pacuta_HTHC_TP3_2527 Pacuta_HTHC_TP3_2527 Pacuta HTHC
## Pacuta_HTHC_TP4_1169 Pacuta_HTHC_TP4_1169 Pacuta HTHC
## Pacuta_HTHC_TP5_1168 Pacuta_HTHC_TP5_1168 Pacuta HTHC
## Pacuta_ATAC_TP5_1059 Pacuta_ATAC_TP5_1059 Pacuta ATAC
## Pacuta_HTHC_TP1_2210 Pacuta_HTHC_TP1_2210 Pacuta HTHC
## Pacuta_HTAC_TP1_1653 Pacuta_HTAC_TP1_1653 Pacuta HTAC
## Pacuta_HTHC_TP6_1721 Pacuta_HTHC_TP6_1721 Pacuta HTHC
## Pacuta_ATAC_TP7_1445 Pacuta_ATAC_TP7_1445 Pacuta ATAC
## Pacuta_ATHC_TP10_1205 Pacuta_ATHC_TP10_1205 Pacuta ATHC
## Pacuta_ATHC_TP10_2550 Pacuta_ATHC_TP10_2550 Pacuta ATHC
## Pacuta_ATHC_TP6_1254 Pacuta_ATHC_TP6_1254 Pacuta ATHC
## Pacuta_HTHC_TP11_2185 Pacuta_HTHC_TP11_2185 Pacuta HTHC
## Pacuta_HTHC_TP5_1415 Pacuta_HTHC_TP5_1415 Pacuta HTHC
## SRR6914151 SRR6914151 Pacuta sediment-only
## SRR6914609 SRR6914609 Pacuta sediment-only
## SRR6914908 SRR6914908 Pacuta heat-only
## SRR6934388 SRR6934388 Pacuta heat-only
## SRR6934542 SRR6934542 Pacuta heat-only
## SRR6935629 SRR6935629 Pacuta heat_with_sediment
## SRR6942678 SRR6942678 Pacuta heat_with_sediment
## SRR6942729 SRR6942729 Pacuta heat_with_sediment
## SRR6951423 SRR6951423 Pacuta control
## SRR6951744 SRR6951744 Pacuta control
## SRR6952431 SRR6952431 Pacuta control
## SRR6963586 SRR6963586 Pacuta sediment-only
## SRR6963878 SRR6963878 Pacuta not_specified
## SRR6963891 SRR6963891 Pacuta sediment-only
## SRR6964364 SRR6964364 Pacuta heat-only
## SRR6986864 SRR6986864 Pacuta heat-only
## SRR6987146 SRR6987146 Pacuta heat-only
## SRR7039808 SRR7039808 Pacuta heat_with_sediment
## SRR7040514 SRR7040514 Pacuta heat_with_sediment
## SRR7041301 SRR7041301 Pacuta heat_with_sediment
## SRR7042978 SRR7042978 Pacuta control
## SRR7043013 SRR7043013 Pacuta control
## SRR7043704 SRR7043704 Pacuta control
## SRR7046161 SRR7046161 Pacuta sediment-only
## SRR7055829 SRR7055829 Pacuta sediment-only
## SRR7058378 SRR7058378 Pacuta sediment-only
## SRR7058566 SRR7058566 Pacuta heat-only
## SRR7058606 SRR7058606 Pacuta heat-only
## SRR7058616 SRR7058616 Pacuta heat-only
## SRR7059699 SRR7059699 Pacuta heat_with_sediment
## SRR7062295 SRR7062295 Pacuta heat_with_sediment
## SRR7062350 SRR7062350 Pacuta heat_with_sediment
## timepoint plugid reef
## Pacuta_ATAC_TP11_1777 TP11 1777 HIMB
## Pacuta_ATAC_TP8_1051 TP8 1051 Reef.11.13
## Pacuta_ATHC_TP4_2733 TP4 2733 Reef.42.43
## Pacuta_ATHC_TP8_1459 TP8 1459 Reef.18
## Pacuta_HTAC_TP3_1642 TP3 1642 HIMB
## Pacuta_HTAC_TP4_1767 TP4 1767 Reef.42.43
## Pacuta_HTAC_TP7_2072 TP7 2072 HIMB
## Pacuta_ATAC_TP11_1103 TP11 1103 Reef.42.43
## Pacuta_ATAC_TP11_2306 TP11 2306 Reef.18
## Pacuta_ATAC_TP3_1041 TP3 1041 Reef.11.13
## Pacuta_ATAC_TP3_1637 TP3 1637 Reef.11.13
## Pacuta_ATAC_TP4_1762 TP4 1762 Reef.42.43
## Pacuta_ATAC_TP7_2413 TP7 2413 Reef.18
## Pacuta_ATAC_TP8_2012 TP8 2012 Reef.42.43
## Pacuta_ATAC_TP9_2357 TP9 2357 Reef.18
## Pacuta_ATHC_TP11_1147 TP11 1147 HIMB
## Pacuta_ATHC_TP3_2534 TP3 2534 Reef.18
## Pacuta_ATHC_TP4_1220 TP4 1220 Lilipuna.Fringe
## Pacuta_ATHC_TP5_2877 TP5 2877 HIMB
## Pacuta_ATHC_TP6_2870 TP6 2870 HIMB
## Pacuta_ATHC_TP7_2878 TP7 2878 HIMB
## Pacuta_ATHC_TP9_1451 TP9 1451 Reef.18
## Pacuta_ATHC_TP9_2873 TP9 2873 HIMB
## Pacuta_HTAC_TP10_2064 TP10 2064 HIMB
## Pacuta_HTAC_TP11_1596 TP11 1596 Reef.42.43
## Pacuta_HTAC_TP1_2414 TP1 2414 Reef.18
## Pacuta_HTAC_TP5_1707 TP5 1707 Reef.11.13
## Pacuta_HTAC_TP6_1466 TP6 1466 Lilipuna.Fringe
## Pacuta_HTAC_TP7_1728 TP7 1728 Reef.18
## Pacuta_HTAC_TP8_2513 TP8 2513 Reef.18
## Pacuta_HTAC_TP9_1696 TP9 1696 Lilipuna.Fringe
## Pacuta_HTHC_TP10_2300 TP10 2300 Reef.18
## Pacuta_HTHC_TP3_1227 TP3 1227 Reef.42.43
## Pacuta_HTHC_TP5_2087 TP5 2087 HIMB
## Pacuta_HTHC_TP6_1138 TP6 1138 HIMB
## Pacuta_HTHC_TP6_1595 TP6 1595 HIMB
## Pacuta_HTHC_TP8_1709 TP8 1709 Lilipuna.Fringe
## Pacuta_HTHC_TP8_2304 TP8 2304 Reef.18
## Pacuta_HTHC_TP9_1131 TP9 1131 HIMB
## Pacuta_HTHC_TP9_2202 TP9 2202 HIMB
## Pacuta_HTHC_TP9_2305 TP9 2305 Reef.18
## Pacuta_ATAC_TP10_1559 TP10 1559 Lilipuna.Fringe
## Pacuta_ATAC_TP10_1641 TP10 1641 HIMB
## Pacuta_ATAC_TP1_2363 TP1 2363 Reef.18
## Pacuta_ATAC_TP3_1471 TP3 1471 Reef.35.36
## Pacuta_ATAC_TP4_1060 TP4 1060 Reef.18
## Pacuta_ATAC_TP4_2002 TP4 2002 Reef.42.43
## Pacuta_ATAC_TP5_1563 TP5 1563 Lilipuna.Fringe
## Pacuta_ATAC_TP5_1757 TP5 1757 Reef.42.43
## Pacuta_ATAC_TP9_1594 TP9 1594 Reef.35.36
## Pacuta_ATHC_TP7_2409 TP7 2409 Lilipuna.Fringe
## Pacuta_ATHC_TP8_2564 TP8 2564 Reef.18
## Pacuta_HTAC_TP10_1536 TP10 1536 Reef.35.36
## Pacuta_HTAC_TP11_1582 TP11 1582 Lilipuna.Fringe
## Pacuta_HTAC_TP11_1647 TP11 1647 HIMB
## Pacuta_HTAC_TP1_2005 TP1 2005 Reef.18
## Pacuta_HTAC_TP3_1617 TP3 1617 Reef.42.43
## Pacuta_HTAC_TP4_1701 TP4 1701 Reef.18
## Pacuta_HTAC_TP8_1765 TP8 1765 Reef.42.43
## Pacuta_HTHC_TP10_1238 TP10 1238 Reef.42.43
## Pacuta_HTHC_TP10_1732 TP10 1732 Lilipuna.Fringe
## Pacuta_HTHC_TP1_1239 TP1 1239 Reef.42.43
## Pacuta_HTHC_TP4_2195 TP4 2195 Reef.42.43
## Pacuta_HTHC_TP7_1090 TP7 1090 Lilipuna.Fringe
## Pacuta_HTHC_TP7_1820 TP7 1820 Reef.11.13
## Pacuta_ATAC_TP1_1043 TP1 1043 Lilipuna.Fringe
## Pacuta_ATAC_TP6_1542 TP6 1542 Lilipuna.Fringe
## Pacuta_ATHC_TP1_2743 TP1 2743 Lilipuna.Fringe
## Pacuta_ATHC_TP3_2750 TP3 2750 Reef.42.43
## Pacuta_HTAC_TP4_1581 TP4 1581 Lilipuna.Fringe
## Pacuta_HTHC_TP4_1343 TP4 1343 Lilipuna.Fringe
## Pacuta_HTHC_TP7_1427 TP7 1427 Lilipuna.Fringe
## Pacuta_HTHC_TP8_1184 TP8 1184 Lilipuna.Fringe
## Pacuta_ATAC_TP10_1159 TP10 1159 Reef.42.43
## Pacuta_ATAC_TP1_1775 TP1 1775 Reef.42.43
## Pacuta_ATAC_TP6_1468 TP6 1468 Reef.35.36
## Pacuta_ATAC_TP8_1755 TP8 1755 Reef.42.43
## Pacuta_ATAC_TP9_1141 TP9 1141 Reef.42.43
## Pacuta_ATHC_TP5_2212 TP5 2212 Reef.35.36
## Pacuta_HTAC_TP6_1744 TP6 1744 Reef.35.36
## Pacuta_HTAC_TP9_1302 TP9 1302 Reef.35.36
## Pacuta_HTAC_TP9_1486 TP9 1486 Reef.11.13
## Pacuta_ATAC_TP6_1050 TP6 1050 Reef.18
## Pacuta_ATAC_TP7_1047 TP7 1047 Lilipuna.Fringe
## Pacuta_ATHC_TP10_2197 TP10 2197 Reef.35.36
## Pacuta_ATHC_TP1_1207 TP1 1207 Reef.11.13
## Pacuta_ATHC_TP11_2668 TP11 2668 Lilipuna.Fringe
## Pacuta_ATHC_TP11_2879 TP11 2879 HIMB
## Pacuta_ATHC_TP1_2977 TP1 2977 Reef.11.13
## Pacuta_ATHC_TP3_1219 TP3 1219 Reef.35.36
## Pacuta_ATHC_TP4_2993 TP4 2993 Reef.11.13
## Pacuta_ATHC_TP5_1296 TP5 1296 Reef.11.13
## Pacuta_ATHC_TP6_2999 TP6 2999 Lilipuna.Fringe
## Pacuta_ATHC_TP7_1281 TP7 1281 Reef.35.36
## Pacuta_ATHC_TP8_2861 TP8 2861 HIMB
## Pacuta_ATHC_TP9_2979 TP9 2979 Reef.35.36
## Pacuta_HTAC_TP10_1225 TP10 1225 HIMB
## Pacuta_HTAC_TP3_2026 TP3 2026 Reef.42.43
## Pacuta_HTAC_TP5_1303 TP5 1303 Reef.35.36
## Pacuta_HTAC_TP5_1571 TP5 1571 Reef.35.36
## Pacuta_HTAC_TP6_1330 TP6 1330 Reef.35.36
## Pacuta_HTAC_TP7_1487 TP7 1487 Lilipuna.Fringe
## Pacuta_HTAC_TP8_1329 TP8 1329 Lilipuna.Fringe
## Pacuta_HTHC_TP11_1416 TP11 1416 Reef.11.13
## Pacuta_HTHC_TP1_1676 TP1 1676 Reef.42.43
## Pacuta_HTHC_TP3_1418 TP3 1418 Lilipuna.Fringe
## Pacuta_HTHC_TP3_2527 TP3 2527 Reef.18
## Pacuta_HTHC_TP4_1169 TP4 1169 Reef.35.36
## Pacuta_HTHC_TP5_1168 TP5 1168 Reef.35.36
## Pacuta_ATAC_TP5_1059 TP5 1059 Reef.11.13
## Pacuta_HTHC_TP1_2210 TP1 2210 Reef.42.43
## Pacuta_HTAC_TP1_1653 TP1 1653 HIMB
## Pacuta_HTHC_TP6_1721 TP6 1721 Lilipuna.Fringe
## Pacuta_ATAC_TP7_1445 TP7 1445 Reef.11.13
## Pacuta_ATHC_TP10_1205 TP10 1205 Reef.35.36
## Pacuta_ATHC_TP10_2550 TP10 2550 Reef.18
## Pacuta_ATHC_TP6_1254 TP6 1254 Reef.42.43
## Pacuta_HTHC_TP11_2185 TP11 2185 HIMB
## Pacuta_HTHC_TP5_1415 TP5 1415 Reef.11.13
## SRR6914151 <NA> RAS1_3 SRA-Singapore-Raffles_Lighthouse
## SRR6914609 <NA> RAS1_2 SRA-Singapore-Raffles_Lighthouse
## SRR6914908 <NA> RH1_1 SRA-Singapore-Raffles_Lighthouse
## SRR6934388 <NA> RH1_2 SRA-Singapore-Raffles_Lighthouse
## SRR6934542 <NA> RH1_3 SRA-Singapore-Raffles_Lighthouse
## SRR6935629 <NA> RHS1_1 SRA-Singapore-Raffles_Lighthouse
## SRR6942678 <NA> RHS1_2 SRA-Singapore-Raffles_Lighthouse
## SRR6942729 <NA> RHS1_3 SRA-Singapore-Raffles_Lighthouse
## SRR6951423 <NA> KA1_1 SRA-Singapore-Kusu_Island
## SRR6951744 <NA> KA1_2 SRA-Singapore-Kusu_Island
## SRR6952431 <NA> KA1_3 SRA-Singapore-Kusu_Island
## SRR6963586 <NA> KAS1_1 SRA-Singapore-Kusu_Island
## SRR6963878 <NA> KAS1_2 SRA-Singapore-Kusu_Island
## SRR6963891 <NA> KAS1_3 SRA-Singapore-Kusu_Island
## SRR6964364 <NA> KH1_1 SRA-Singapore-Kusu_Island
## SRR6986864 <NA> KH1_2 SRA-Singapore-Kusu_Island
## SRR6987146 <NA> KH1_3 SRA-Singapore-Kusu_Island
## SRR7039808 <NA> KHS1_1 SRA-Singapore-Kusu_Island
## SRR7040514 <NA> KHS1_2 SRA-Singapore-Kusu_Island
## SRR7041301 <NA> KHS1_3 SRA-Singapore-Kusu_Island
## SRR7042978 <NA> SA1_1 SRA-Singapore-St_Johns_Island
## SRR7043013 <NA> SA1_2 SRA-Singapore-St_Johns_Island
## SRR7043704 <NA> SA1_3 SRA-Singapore-St_Johns_Island
## SRR7046161 <NA> SAS1_1 SRA-Singapore-St_Johns_Island
## SRR7055829 <NA> SAS1_2 SRA-Singapore-St_Johns_Island
## SRR7058378 <NA> SAS1_3 SRA-Singapore-St_Johns_Island
## SRR7058566 <NA> SH1_1 SRA-Singapore-St_Johns_Island
## SRR7058606 <NA> SH1_2 SRA-Singapore-St_Johns_Island
## SRR7058616 <NA> SH1_3 SRA-Singapore-St_Johns_Island
## SRR7059699 <NA> SHS1_1 SRA-Singapore-St_Johns_Island
## SRR7062295 <NA> SHS1_2 SRA-Singapore-St_Johns_Island
## SRR7062350 <NA> SHS1_3_B2 SRA-Singapore-St_Johns_Island
## reef_color ploidy ploidy_color
## Pacuta_ATAC_TP11_1777 #b35806 3 #d95f02
## Pacuta_ATAC_TP8_1051 #fee0b6 3 #d95f02
## Pacuta_ATHC_TP4_2733 #542788 3 #d95f02
## Pacuta_ATHC_TP8_1459 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP3_1642 #b35806 3 #d95f02
## Pacuta_HTAC_TP4_1767 #542788 3 #d95f02
## Pacuta_HTAC_TP7_2072 #b35806 3 #d95f02
## Pacuta_ATAC_TP11_1103 #542788 3 #d95f02
## Pacuta_ATAC_TP11_2306 #d8daeb 3 #d95f02
## Pacuta_ATAC_TP3_1041 #fee0b6 3 #d95f02
## Pacuta_ATAC_TP3_1637 #fee0b6 3 #d95f02
## Pacuta_ATAC_TP4_1762 #542788 3 #d95f02
## Pacuta_ATAC_TP7_2413 #d8daeb 3 #d95f02
## Pacuta_ATAC_TP8_2012 #542788 3 #d95f02
## Pacuta_ATAC_TP9_2357 #d8daeb 3 #d95f02
## Pacuta_ATHC_TP11_1147 #b35806 3 #d95f02
## Pacuta_ATHC_TP3_2534 #d8daeb 3 #d95f02
## Pacuta_ATHC_TP4_1220 #f1a340 3 #d95f02
## Pacuta_ATHC_TP5_2877 #b35806 3 #d95f02
## Pacuta_ATHC_TP6_2870 #b35806 3 #d95f02
## Pacuta_ATHC_TP7_2878 #b35806 3 #d95f02
## Pacuta_ATHC_TP9_1451 #d8daeb 3 #d95f02
## Pacuta_ATHC_TP9_2873 #b35806 3 #d95f02
## Pacuta_HTAC_TP10_2064 #b35806 3 #d95f02
## Pacuta_HTAC_TP11_1596 #542788 3 #d95f02
## Pacuta_HTAC_TP1_2414 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP5_1707 #fee0b6 3 #d95f02
## Pacuta_HTAC_TP6_1466 #f1a340 3 #d95f02
## Pacuta_HTAC_TP7_1728 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP8_2513 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP9_1696 #f1a340 3 #d95f02
## Pacuta_HTHC_TP10_2300 #d8daeb 3 #d95f02
## Pacuta_HTHC_TP3_1227 #542788 3 #d95f02
## Pacuta_HTHC_TP5_2087 #b35806 3 #d95f02
## Pacuta_HTHC_TP6_1138 #b35806 3 #d95f02
## Pacuta_HTHC_TP6_1595 #b35806 3 #d95f02
## Pacuta_HTHC_TP8_1709 #f1a340 3 #d95f02
## Pacuta_HTHC_TP8_2304 #d8daeb 3 #d95f02
## Pacuta_HTHC_TP9_1131 #b35806 3 #d95f02
## Pacuta_HTHC_TP9_2202 #b35806 3 #d95f02
## Pacuta_HTHC_TP9_2305 #d8daeb 3 #d95f02
## Pacuta_ATAC_TP10_1559 #f1a340 3 #d95f02
## Pacuta_ATAC_TP10_1641 #b35806 3 #d95f02
## Pacuta_ATAC_TP1_2363 #d8daeb 3 #d95f02
## Pacuta_ATAC_TP3_1471 #998ec3 3 #d95f02
## Pacuta_ATAC_TP4_1060 #d8daeb 3 #d95f02
## Pacuta_ATAC_TP4_2002 #542788 3 #d95f02
## Pacuta_ATAC_TP5_1563 #f1a340 3 #d95f02
## Pacuta_ATAC_TP5_1757 #542788 3 #d95f02
## Pacuta_ATAC_TP9_1594 #998ec3 3 #d95f02
## Pacuta_ATHC_TP7_2409 #f1a340 3 #d95f02
## Pacuta_ATHC_TP8_2564 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP10_1536 #998ec3 3 #d95f02
## Pacuta_HTAC_TP11_1582 #f1a340 3 #d95f02
## Pacuta_HTAC_TP11_1647 #b35806 3 #d95f02
## Pacuta_HTAC_TP1_2005 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP3_1617 #542788 3 #d95f02
## Pacuta_HTAC_TP4_1701 #d8daeb 3 #d95f02
## Pacuta_HTAC_TP8_1765 #542788 3 #d95f02
## Pacuta_HTHC_TP10_1238 #542788 3 #d95f02
## Pacuta_HTHC_TP10_1732 #f1a340 3 #d95f02
## Pacuta_HTHC_TP1_1239 #542788 3 #d95f02
## Pacuta_HTHC_TP4_2195 #542788 3 #d95f02
## Pacuta_HTHC_TP7_1090 #f1a340 3 #d95f02
## Pacuta_HTHC_TP7_1820 #fee0b6 3 #d95f02
## Pacuta_ATAC_TP1_1043 #f1a340 3 #d95f02
## Pacuta_ATAC_TP6_1542 #f1a340 3 #d95f02
## Pacuta_ATHC_TP1_2743 #f1a340 3 #d95f02
## Pacuta_ATHC_TP3_2750 #542788 3 #d95f02
## Pacuta_HTAC_TP4_1581 #f1a340 3 #d95f02
## Pacuta_HTHC_TP4_1343 #f1a340 3 #d95f02
## Pacuta_HTHC_TP7_1427 #f1a340 3 #d95f02
## Pacuta_HTHC_TP8_1184 #f1a340 3 #d95f02
## Pacuta_ATAC_TP10_1159 #542788 2 #1b9e77
## Pacuta_ATAC_TP1_1775 #542788 2 #1b9e77
## Pacuta_ATAC_TP6_1468 #998ec3 2 #1b9e77
## Pacuta_ATAC_TP8_1755 #542788 2 #1b9e77
## Pacuta_ATAC_TP9_1141 #542788 2 #1b9e77
## Pacuta_ATHC_TP5_2212 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP6_1744 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP9_1302 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP9_1486 #fee0b6 2 #1b9e77
## Pacuta_ATAC_TP6_1050 #d8daeb 2 #1b9e77
## Pacuta_ATAC_TP7_1047 #f1a340 2 #1b9e77
## Pacuta_ATHC_TP10_2197 #998ec3 2 #1b9e77
## Pacuta_ATHC_TP1_1207 #fee0b6 2 #1b9e77
## Pacuta_ATHC_TP11_2668 #f1a340 2 #1b9e77
## Pacuta_ATHC_TP11_2879 #b35806 2 #1b9e77
## Pacuta_ATHC_TP1_2977 #fee0b6 2 #1b9e77
## Pacuta_ATHC_TP3_1219 #998ec3 2 #1b9e77
## Pacuta_ATHC_TP4_2993 #fee0b6 2 #1b9e77
## Pacuta_ATHC_TP5_1296 #fee0b6 2 #1b9e77
## Pacuta_ATHC_TP6_2999 #f1a340 2 #1b9e77
## Pacuta_ATHC_TP7_1281 #998ec3 2 #1b9e77
## Pacuta_ATHC_TP8_2861 #b35806 2 #1b9e77
## Pacuta_ATHC_TP9_2979 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP10_1225 #b35806 2 #1b9e77
## Pacuta_HTAC_TP3_2026 #542788 2 #1b9e77
## Pacuta_HTAC_TP5_1303 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP5_1571 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP6_1330 #998ec3 2 #1b9e77
## Pacuta_HTAC_TP7_1487 #f1a340 2 #1b9e77
## Pacuta_HTAC_TP8_1329 #f1a340 2 #1b9e77
## Pacuta_HTHC_TP11_1416 #fee0b6 2 #1b9e77
## Pacuta_HTHC_TP1_1676 #542788 2 #1b9e77
## Pacuta_HTHC_TP3_1418 #f1a340 2 #1b9e77
## Pacuta_HTHC_TP3_2527 #d8daeb 2 #1b9e77
## Pacuta_HTHC_TP4_1169 #998ec3 2 #1b9e77
## Pacuta_HTHC_TP5_1168 #998ec3 2 #1b9e77
## Pacuta_ATAC_TP5_1059 #fee0b6 2 #1b9e77
## Pacuta_HTHC_TP1_2210 #542788 2 #1b9e77
## Pacuta_HTAC_TP1_1653 #b35806 2 #1b9e77
## Pacuta_HTHC_TP6_1721 #f1a340 2 #1b9e77
## Pacuta_ATAC_TP7_1445 #fee0b6 2 #1b9e77
## Pacuta_ATHC_TP10_1205 #998ec3 2 #1b9e77
## Pacuta_ATHC_TP10_2550 #d8daeb 2 #1b9e77
## Pacuta_ATHC_TP6_1254 #542788 3 #d95f02
## Pacuta_HTHC_TP11_2185 #b35806 3 #d95f02
## Pacuta_HTHC_TP5_1415 #fee0b6 2 #1b9e77
## SRR6914151 #9d529e 2 #01665e
## SRR6914609 #9d529e 2 #01665e
## SRR6914908 #9d529e 2 #01665e
## SRR6934388 #9d529e 2 #01665e
## SRR6934542 #9d529e 2 #01665e
## SRR6935629 #9d529e 2 #01665e
## SRR6942678 #9d529e 2 #01665e
## SRR6942729 #9d529e 2 #01665e
## SRR6951423 #bc80bd 2 #01665e
## SRR6951744 #bc80bd 2 #01665e
## SRR6952431 #bc80bd 2 #01665e
## SRR6963586 #bc80bd 2 #01665e
## SRR6963878 #bc80bd 2 #01665e
## SRR6963891 #bc80bd 2 #01665e
## SRR6964364 #bc80bd 2 #01665e
## SRR6986864 #bc80bd 2 #01665e
## SRR6987146 #bc80bd 2 #01665e
## SRR7039808 #bc80bd 2 #01665e
## SRR7040514 #bc80bd 2 #01665e
## SRR7041301 #bc80bd 2 #01665e
## SRR7042978 #e1cbe1 2 #01665e
## SRR7043013 #e1cbe1 2 #01665e
## SRR7043704 #e1cbe1 2 #01665e
## SRR7046161 #e1cbe1 2 #01665e
## SRR7055829 #e1cbe1 2 #01665e
## SRR7058378 #e1cbe1 2 #01665e
## SRR7058566 #e1cbe1 2 #01665e
## SRR7058606 #e1cbe1 2 #01665e
## SRR7058616 #e1cbe1 2 #01665e
## SRR7059699 #e1cbe1 2 #01665e
## SRR7062295 #e1cbe1 2 #01665e
## SRR7062350 #e1cbe1 2 #01665e
## group group_color
## Pacuta_ATAC_TP11_1777 Group1 #1f78b4
## Pacuta_ATAC_TP8_1051 Group1 #1f78b4
## Pacuta_ATHC_TP4_2733 Group1 #1f78b4
## Pacuta_ATHC_TP8_1459 Group1 #1f78b4
## Pacuta_HTAC_TP3_1642 Group1 #1f78b4
## Pacuta_HTAC_TP4_1767 Group1 #1f78b4
## Pacuta_HTAC_TP7_2072 Group1 #1f78b4
## Pacuta_ATAC_TP11_1103 Group2 #33a02c
## Pacuta_ATAC_TP11_2306 Group2 #33a02c
## Pacuta_ATAC_TP3_1041 Group2 #33a02c
## Pacuta_ATAC_TP3_1637 Group2 #33a02c
## Pacuta_ATAC_TP4_1762 Group2 #33a02c
## Pacuta_ATAC_TP7_2413 Group2 #33a02c
## Pacuta_ATAC_TP8_2012 Group2 #33a02c
## Pacuta_ATAC_TP9_2357 Group2 #33a02c
## Pacuta_ATHC_TP11_1147 Group2 #33a02c
## Pacuta_ATHC_TP3_2534 Group2 #33a02c
## Pacuta_ATHC_TP4_1220 Group2 #33a02c
## Pacuta_ATHC_TP5_2877 Group2 #33a02c
## Pacuta_ATHC_TP6_2870 Group2 #33a02c
## Pacuta_ATHC_TP7_2878 Group2 #33a02c
## Pacuta_ATHC_TP9_1451 Group2 #33a02c
## Pacuta_ATHC_TP9_2873 Group2 #33a02c
## Pacuta_HTAC_TP10_2064 Group2 #33a02c
## Pacuta_HTAC_TP11_1596 Group2 #33a02c
## Pacuta_HTAC_TP1_2414 Group2 #33a02c
## Pacuta_HTAC_TP5_1707 Group2 #33a02c
## Pacuta_HTAC_TP6_1466 Group2 #33a02c
## Pacuta_HTAC_TP7_1728 Group2 #33a02c
## Pacuta_HTAC_TP8_2513 Group2 #33a02c
## Pacuta_HTAC_TP9_1696 Group2 #33a02c
## Pacuta_HTHC_TP10_2300 Group2 #33a02c
## Pacuta_HTHC_TP3_1227 Group2 #33a02c
## Pacuta_HTHC_TP5_2087 Group2 #33a02c
## Pacuta_HTHC_TP6_1138 Group2 #33a02c
## Pacuta_HTHC_TP6_1595 Group2 #33a02c
## Pacuta_HTHC_TP8_1709 Group2 #33a02c
## Pacuta_HTHC_TP8_2304 Group2 #33a02c
## Pacuta_HTHC_TP9_1131 Group2 #33a02c
## Pacuta_HTHC_TP9_2202 Group2 #33a02c
## Pacuta_HTHC_TP9_2305 Group2 #33a02c
## Pacuta_ATAC_TP10_1559 Group3 #c51b7d
## Pacuta_ATAC_TP10_1641 Group3 #c51b7d
## Pacuta_ATAC_TP1_2363 Group3 #c51b7d
## Pacuta_ATAC_TP3_1471 Group3 #c51b7d
## Pacuta_ATAC_TP4_1060 Group3 #c51b7d
## Pacuta_ATAC_TP4_2002 Group3 #c51b7d
## Pacuta_ATAC_TP5_1563 Group3 #c51b7d
## Pacuta_ATAC_TP5_1757 Group3 #c51b7d
## Pacuta_ATAC_TP9_1594 Group3 #c51b7d
## Pacuta_ATHC_TP7_2409 Group3 #c51b7d
## Pacuta_ATHC_TP8_2564 Group3 #c51b7d
## Pacuta_HTAC_TP10_1536 Group3 #c51b7d
## Pacuta_HTAC_TP11_1582 Group3 #c51b7d
## Pacuta_HTAC_TP11_1647 Group3 #c51b7d
## Pacuta_HTAC_TP1_2005 Group3 #c51b7d
## Pacuta_HTAC_TP3_1617 Group3 #c51b7d
## Pacuta_HTAC_TP4_1701 Group3 #c51b7d
## Pacuta_HTAC_TP8_1765 Group3 #c51b7d
## Pacuta_HTHC_TP10_1238 Group3 #c51b7d
## Pacuta_HTHC_TP10_1732 Group3 #c51b7d
## Pacuta_HTHC_TP1_1239 Group3 #c51b7d
## Pacuta_HTHC_TP4_2195 Group3 #c51b7d
## Pacuta_HTHC_TP7_1090 Group3 #c51b7d
## Pacuta_HTHC_TP7_1820 Group3 #c51b7d
## Pacuta_ATAC_TP1_1043 Group4 #6a3d9a
## Pacuta_ATAC_TP6_1542 Group4 #6a3d9a
## Pacuta_ATHC_TP1_2743 Group4 #6a3d9a
## Pacuta_ATHC_TP3_2750 Group4 #6a3d9a
## Pacuta_HTAC_TP4_1581 Group4 #6a3d9a
## Pacuta_HTHC_TP4_1343 Group4 #6a3d9a
## Pacuta_HTHC_TP7_1427 Group4 #6a3d9a
## Pacuta_HTHC_TP8_1184 Group4 #6a3d9a
## Pacuta_ATAC_TP10_1159 Group5 #ff7f00
## Pacuta_ATAC_TP1_1775 Group5 #ff7f00
## Pacuta_ATAC_TP6_1468 Group5 #ff7f00
## Pacuta_ATAC_TP8_1755 Group5 #ff7f00
## Pacuta_ATAC_TP9_1141 Group5 #ff7f00
## Pacuta_ATHC_TP5_2212 Group5 #ff7f00
## Pacuta_HTAC_TP6_1744 Group5 #ff7f00
## Pacuta_HTAC_TP9_1302 Group5 #ff7f00
## Pacuta_HTAC_TP9_1486 Group5 #ff7f00
## Pacuta_ATAC_TP6_1050 Group6 #e31a1c
## Pacuta_ATAC_TP7_1047 Group6 #e31a1c
## Pacuta_ATHC_TP10_2197 Group6 #e31a1c
## Pacuta_ATHC_TP1_1207 Group6 #e31a1c
## Pacuta_ATHC_TP11_2668 Group6 #e31a1c
## Pacuta_ATHC_TP11_2879 Group6 #e31a1c
## Pacuta_ATHC_TP1_2977 Group6 #e31a1c
## Pacuta_ATHC_TP3_1219 Group6 #e31a1c
## Pacuta_ATHC_TP4_2993 Group6 #e31a1c
## Pacuta_ATHC_TP5_1296 Group6 #e31a1c
## Pacuta_ATHC_TP6_2999 Group6 #e31a1c
## Pacuta_ATHC_TP7_1281 Group6 #e31a1c
## Pacuta_ATHC_TP8_2861 Group6 #e31a1c
## Pacuta_ATHC_TP9_2979 Group6 #e31a1c
## Pacuta_HTAC_TP10_1225 Group6 #e31a1c
## Pacuta_HTAC_TP3_2026 Group6 #e31a1c
## Pacuta_HTAC_TP5_1303 Group6 #e31a1c
## Pacuta_HTAC_TP5_1571 Group6 #e31a1c
## Pacuta_HTAC_TP6_1330 Group6 #e31a1c
## Pacuta_HTAC_TP7_1487 Group6 #e31a1c
## Pacuta_HTAC_TP8_1329 Group6 #e31a1c
## Pacuta_HTHC_TP11_1416 Group6 #e31a1c
## Pacuta_HTHC_TP1_1676 Group6 #e31a1c
## Pacuta_HTHC_TP3_1418 Group6 #e31a1c
## Pacuta_HTHC_TP3_2527 Group6 #e31a1c
## Pacuta_HTHC_TP4_1169 Group6 #e31a1c
## Pacuta_HTHC_TP5_1168 Group6 #e31a1c
## Pacuta_ATAC_TP5_1059 Group7 #b15928
## Pacuta_HTHC_TP1_2210 Group7 #b15928
## Pacuta_HTAC_TP1_1653 Group8 #000000
## Pacuta_HTHC_TP6_1721 Group8 #000000
## Pacuta_ATAC_TP7_1445 Ungroup #808080
## Pacuta_ATHC_TP10_1205 Ungroup #808080
## Pacuta_ATHC_TP10_2550 Ungroup #808080
## Pacuta_ATHC_TP6_1254 Ungroup #808080
## Pacuta_HTHC_TP11_2185 Ungroup #808080
## Pacuta_HTHC_TP5_1415 Ungroup #808080
## SRR6914151 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6914609 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6914908 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6934388 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6934542 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6935629 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6942678 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6942729 SRA-Singapore-Raffles_Lighthouse #9d529e
## SRR6951423 SRA-Singapore-Kusu_Island #bc80bd
## SRR6951744 SRA-Singapore-Kusu_Island #bc80bd
## SRR6952431 SRA-Singapore-Kusu_Island #bc80bd
## SRR6963586 SRA-Singapore-Kusu_Island #bc80bd
## SRR6963878 SRA-Singapore-Kusu_Island #bc80bd
## SRR6963891 SRA-Singapore-Kusu_Island #bc80bd
## SRR6964364 SRA-Singapore-Kusu_Island #bc80bd
## SRR6986864 SRA-Singapore-Kusu_Island #bc80bd
## SRR6987146 SRA-Singapore-Kusu_Island #bc80bd
## SRR7039808 SRA-Singapore-Kusu_Island #bc80bd
## SRR7040514 SRA-Singapore-Kusu_Island #bc80bd
## SRR7041301 SRA-Singapore-Kusu_Island #bc80bd
## SRR7042978 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7043013 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7043704 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7046161 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7055829 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7058378 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7058566 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7058606 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7058616 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7059699 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7062295 SRA-Singapore-St_Johns_Island #e1cbe1
## SRR7062350 SRA-Singapore-St_Johns_Island #e1cbe1
Load pairwise percent shared SNP results and convert if from one line per pair format into a symetric matrix uisng the xtabs function.
pairwise_percent_shared <- read.table("GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.tsv", sep='\t', header=T)
pairwise_percent_shared.matrix <- xtabs(match_perc ~ ind1 + ind2, data=pairwise_percent_shared)
Process the simScore data ready for plotting (i.e., cluster samples based on computed distance and construct a dendrogram of the relationship).
# Make a copy of input matrix
tmp.mat <- pairwise_percent_shared.matrix
# Generate clusters from the allelic similarity scores matrix
tmp.mat.dist <- dist(tmp.mat, method="euclidean")
tmp.mat.hclust <- hclust(tmp.mat.dist, method="complete")
# Get sample colors for sidebar in the same order as the matrix
Rcols <- samples.info[rownames(tmp.mat),]$group_color
Ccols <- samples.info[colnames(tmp.mat),]$group_color
# Get min and max values of matrix
tmp.mat.min <- min(tmp.mat); tmp.mat.min
## [1] 72.8
tmp.mat.max <- max(tmp.mat); tmp.mat.max
## [1] 100
Plot clustering results and write dendrogram to file.
simScore.dendro <- as.dendrogram(tmp.mat.hclust)
write.dendrogram(simScore.dendro, "cluster_dendrogram.tre", edges=TRUE)
plot(tmp.mat.hclust)
Write ordered matrix to file incase we want it later.
tmp.mat.order <- dendro_data(simScore.dendro, type="rectangle")[["labels"]][["label"]]
tmp.mat.ordered <- tmp.mat[
order(match(rownames(tmp.mat), rev(tmp.mat.order))),
order(match(colnames(tmp.mat), tmp.mat.order))
]
write.table(as.matrix(tmp.mat.ordered),
"GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.matrix.tsv",
sep='\t', quote=FALSE,
row.names=TRUE, col.names=TRUE)
Plot simScores heatmap.
par(cex.main=0.7, cex.lab=0.9, cex.axis=0.9) # Change the font size of the legend title, labels and axis
heatmap.2(x=tmp.mat,
Rowv = simScore.dendro,
Colv = simScore.dendro,
col=cividis(length(seq(70, 100, 0.1))-1),
breaks=seq(70, 100, 0.1),
trace="none", # Dont draw "trace" line
key=TRUE, # Show color-key
margins=c(8,8), # Numeric vector of length 2 containing the margins for column and row names, respectively.
ColSideColors=Ccols,
RowSideColors=Rcols,
offsetRow=0,
offsetCol=0,
cexRow=cexSize, # Positive numbers, used as cex.axis in for the row or column axis labeling.
cexCol=cexSize,
cellnote=formatC(tmp.mat, big.mark=","),
notecex=0.1,
)